CRISPRseek

Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

Bioconductor version: Development (3.0)

The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. This package leverages Biostrings and BSgenome packages.

Author: Lihua Julie Zhu, Benjamin R. Holmes, Neil Aronin and Michael Brodsky

Maintainer: Lihua Julie Zhu <julie.zhu at umassmed.edu>

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("CRISPRseek")

Citation (from within R, enter citation("CRISPRseek")):

Documentation

PDF R Script CRISPRseek Vignette
PDF   Reference Manual

Details

biocViews GeneRegulation, SequenceMatching, Software
Version 1.1.6
In Bioconductor since BioC 2.14 (R-3.1)
License GPL (>= 2)
Depends R (>= 3.0.1), BiocGenerics, Biostrings, BSgenome
Imports
Suggests RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source CRISPRseek_1.1.6.tar.gz
Windows Binary CRISPRseek_1.1.5.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) CRISPRseek_1.1.5.tgz
Mac OS X 10.9 (Mavericks) CRISPRseek_1.1.5.tgz
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